Immune Repertoire Analysis
with Vidjil

Rennes (France) + online, 22-23 May 2024

V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies, and in leukemia, are used to quantify the minimal residual disease during patient follow-up. High-throughput sequencing (NGS/HTS) now enables the deep sequencing of lymphoid populations. With dedicated Rep-Seq bioinformatics methods and software, clinicians and researchers can now qualify and sometimes quantify the heterogeneity of these lymphoid populations.

This sixth workshop is intended for users and developers of Vidjil, to share experience, protocols and results, to raise questions and decide development priorities, and possibly to set up new collaborations between biologists and bioinformaticians. The workshop includes hematology, immunology and bioinformatics talks from an invited speaker and from the users and developers of Vidjil, and practical hands-on sessions on participant data. The registration is free but mandatory, and a remote participation to some of the sessions is possible.
The Vidjil Workshop usually takes place every 18 months. The previous workshops (2016, 2017, 2019, 2020, 2022) gathered at each edition between 30 and 40 scientists from 5 to 7 countries.
The 2024 edition have gathered 40 people from Belgium, Brazil, France, Italy, Lithuania, Norway, Sweden, Switzerland, UK, and USA.

▶️ remote Hybrid participation. The 2024 edition was in Rennes. However, it was also possible to follow remotely part of the workshop.


The workshop includes an invited talk, hematology and bioinformatics talks from the users and developers of Vidjil, and practical hands-on sessions on participant data. We expect that one participant from each group will do a short presentation of his research or clinical work, and, if applicable, of the results obtained with Vidjil or with other software.

For the practical sessions, the participants are invited to bring a laptop and some of their NGS data (fasta / fastq / fastq.gz files). The data can also be uploaded before the workshop into user accounts on before the workshop. We also provide public test data for the people who do not currently have their own NGS Rep-Seq data.

Wednesday 22 May

9:00 – 9:45 Registration, coffee
9:45 – 10:00 Introduction - [Video]
10:00 – 11:00 Keynote talk: Steve Genebrier ▶️ remote
MOBIDIC (MicrOenvironment and B-cell: Immunopathology cell DIfferentiation and Cancer), Univ. Rennes
Adaptive immune receptor repertoires: an immunologist perspective
[Video] - [Slides]
11:15 – 12:15 Talks: Algorithmics and bioinformatics: a tour of the Vidjil platform ▶️ remote
  • Introduction to the Vidjil platform [Video]
  • New and advanced features [Video]
12:30 – 14:00 Lunch break
14:00 – 15:00 Talks: Immunology and Hematology (1) ▶️ remote
15:00 – 16:30 Practical sessions 1
  • Usage of the Vidjil Web platform, analysis of participant and/or public data
  • (both tutorial and advanced usage)
17:00 – 17:30 Talks: Bioinformatics software ▶️ remote
  • Mikaël Salson, Processing VDJ recombinations still faster [Video]
  • Mathieu Giraud, the VidjilNet consortium [Video]
19:30 Dinner at La Réserve, 36-38 rue de la Visitation, 35 000 Rennes

Thursday 23 May

9:00 – 10:30 Talks: Immunology and Hematology (2)▶️ remote
  • Aurélie Caye-Eude (CHU Paris, Robert Debré 🇫🇷) [Video] [Slides]
  • Baptiste Guey (CHUV, Lausanne 🇨🇭) [Video]
  • Emmanuelle Kabongo Kanjinga (UZ Brussels 🇧🇪) [Video] [Slides]
  • Yannick Le Bris (CHU Nantes 🇫🇷)
  • Marie-Hélène Delfau (CHU Paris, Henri Mondor 🇫🇷) [Video] [Slides]
11:00 – 12:30 Practical session 2
12:30 – 13:30 Lunch break
13:30 – 15:00 Round table
  • Discussion on most wanted features, development priorities
  • Meeting of the Scientific and Technic Committee
15:00 – 15:30 Conclusion


The workshop is sponsored by the VidjilNet consortium at Inria. There is no registration fee but it is mandatory to register. To register, please copy, paste and fill the following lines into an email to Clément, Florian, Mathieu and Mikaël :

First name: 
Last name: 

I will be present in Rennes:
    [ ] Both days
    [ ] Wednesday 22 May 2024
    [ ] Thursday 23 May 2024

[ ] I will attend the workshop remotely

My usage of Vidjil:
    [ ] I use Vidjil at least once a month
    [ ] I use Vidjil occasionally
    [ ] I am a new user or I don't use Vidjil

The two lunches (22 and 23 May) and the dinner of the evening of the 22 May are free for registered participants.


Dmitry Djcuce (source: Wikimedia Commons)

Practical information in Rennes

The workshop takes place at Université de Rennes on the Beaulieu campus, in the PNRB building. To go the the PNRB, take the C4 or C6 bus and stop at Les Préales.


The workshop is organized by Clément Chesnin, Mathieu Giraud, Mikaël Salson, Florian Thonier, from CRIStAL, Inria and the VidjilNet consortium.